The present inventions relate to the field of computer systems. More specifically, in one embodiment the invention provides a computer-aided engineering system that generates the design of sequence arrays on a substrate, as well as the design of lithographic masks therefor.
Devices and computer systems for forming and using arrays of materials on a substrate are known. For example, PCT application WO92/10588, incorporated herein by reference for all purposes, describes techniques for sequencing nucleic acids and other materials. Such materials may be formed in arrays according to the methods of, for example, the pioneering techniques disclosed in U.S. Pat. No. 5,143,854, also incorporated herein by reference for all purposes. According to one aspect of the techniques described therein, an array of probes such as nucleic acids are fabricated at known locations on a chip. A labelled biological material such as another nucleic acid is contacted with the chip. Based upon the locations where the biological material binds to the chip, it becomes possible to extract information such as the monomer sequence of, for example, DNA or RNA. Such systems have been used to form, for example, arrays of DNA that may be used to study and detect mutations relevant to the detection of cystic fibrosis, detection of mutations in the P53 gene (relevant to certain cancers), HIV detection, and other genetic characteristics. Exemplary applications of such systems are provided in U.S. Ser. No. 08/143,312 abandoned, (Attorney docket no. 16528X-41/1046), and U.S. Pat. No. 5,288,514, incorporated herein by reference for all purposes.
Such techniques have met with substantial success, and in fact are considered pioneering in the industry. Certain challenges have been met, however, in the process of gathering, assimilating, and using the huge amounts of information now made available by these dramatically improved techniques. Existing computer systems in particular have been found to be wanting in their ability to design, form, assimilate, and process the vast amount of information now used and made available by these pioneering technologies.
Improved computer systems and methods for operating such computer systems are needed to design and form arrays of biological materials.